Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance

Abstract Background Population differentiation is the result of demographic and evolutionary forces. Whole genome datasets from the 1000 Genomes Project (October 2012) provide an unbiased view of genetic variation across populations from Europe, Asia, Africa and the Americas. Common population-specific SNPs (MAF > 0.05) reflect a deep history and may have important consequences for health and wellbeing. Their interpretation is contextualised by currently available genome data. Results The identification of common population-specific (CPS) variants (SNPs and SSV) is influenced by admixture and the sample size under investigation. Nine of the populations in the 1000 Genomes Project (2 African, 2 Asian (including a merged Chinese group) and 5 European) revealed that the African populations (LWK and YRI), followed by the Japanese (JPT) have the highest number of CPS SNPs, in concordance with their histories and given the populations studied. Using two methods, sliding 50-SNP and 5-kb windows, the CPS SNPs showed distinct clustering across large genome segments and little overlap of clusters between populations. iHS enrichment score and the population branch statistic (PBS) analyses suggest that selective sweeps are unlikely to account for the clustering and population specificity. Of interest is the association of clusters close to recombination hotspots. Functional analysis of genes associated with the CPS SNPs revealed over-representation of genes in pathways associated with neuronal development, including axonal guidance signalling and CREB signalling in neurones. Conclusions Common population-specific SNPs are non-randomly distributed throughout the genome and are significantly associated with recombination hotspots. Since the variant alleles of most CPS SNPs are the derived allele, they likely arose in the specific population after a split from a common ancestor. Their proximity to genes involved in specific pathways, including neuronal development, suggests evolutionary plasticity of selected genomic regions. Contrary to expectation, selective sweeps did not play a large role in the persistence of population-specific variation. This suggests a stochastic process towards population-specific variation which reflects demographic histories and may have some interesting implications for health and susceptibility to disease

Leaf trichomes and foliar chemistry mediate defence against glasshouse thrips; Heliothrips haemorrhoidalis (Bouché) in Rhododendron simsii

Herbivore defence mechanisms are a costly diversion of resources away from growth and reproduction. Thus time-limited and tissue specific expression in critical plant parts is more efficient as defined by optimal defence theory. Surprisingly little is known about Rhododendron herbivore defence but it may be mediated by combined chemical and physical mechanisms. Rhododendron simsii Planch. survives cyclic infestations of a leaf-feeding thrips, Heliothrips haemorrhoidalis, which severely damage mature leaves but avoid terminal young leaves suggesting specific, localised defence expression. We examined correlations between the distribution of thrips and feeding damage with density of trichomes and the concentration of the diterpenoid, grayanotoxin I, a compound implicated in but not previously reported to meditate invertebrate defence in Rhododendron. Our data show that as leaves matured the number of thrips and area of feeding damage increased as trichome density and grayanotoxin I concentration decreased, this inverse correlation 10 suggesting trichomes and grayanotoxin I mediate defence in younger leaf tissue. Grayanotoxin I was tested against H. haemorrhoidalis and was toxic to immature life stages and repellent to the adult thrips, reducing numbers of first instars emerging on leaves when applied at ecologically relevant concentrations. This work demonstrates that the pattern of defensive traits in foliage of a species of Rhododendron is key to its ability to tolerate cyclic infestations of a generalist herbivore, effectively conserving vital tissues required for growth and reproduction

100 Years of Scientific Evolution of Work and Organizational Psychology: A Bibliometric Network Analysis From 1919 to 2019

In this study, we explore a 100 years of Work and Organizational Psychology (WOP). To do this, we carry out a bibliometric performance and network analysis (BPNA) to understand the evolution structure and the most important themes in the field of study. To perform the BNPA, 8,966 documents published since 1919 were exported from the Web of Science and Scopus databases. The SciMAT software was used to process data and to create the evolution structure, the strategic diagram, and the thematic network structure of the strategic themes of the field of WOP. We identified 29 strategic clusters and discuss the most important themes (motor themes) and their relationship with other clusters. This research presents the complete evolution of the field of study, identifying emerging themes and others with a high degree of development. We hope that this work will support researchers and future research in the field of WOP

Risk factors for Coronavirus disease 2019 (Covid-19) death in a population cohort study from the Western Cape province, South Africa

Risk factors for coronavirus disease 2019 (COVID-19) death in sub-Saharan Africa and the effects of human immunodeficiency virus (HIV) and tuberculosis on COVID-19 outcomes are unknown. We conducted a population cohort study using linked data from adults attending public-sector health facilities in the Western Cape, South Africa. We used Cox proportional hazards models, adjusted for age, sex, location, and comorbidities, to examine the associations between HIV, tuberculosis, and COVID-19 death from 1 March to 9 June 2020 among (1) public-sector “active patients” (≥1 visit in the 3 years before March 2020); (2) laboratory-diagnosed COVID-19 cases; and (3) hospitalized COVID-19 cases. We calculated the standardized mortality ratio (SMR) for COVID-19, comparing adults living with and without HIV using modeled population estimates.Among 3 460 932 patients (16% living with HIV), 22 308 were diagnosed with COVID-19, of whom 625 died. COVID19 death was associated with male sex, increasing age, diabetes, hypertension, and chronic kidney disease. HIV was associated with COVID-19 mortality (adjusted hazard ratio [aHR], 2.14; 95% confidence interval [CI], 1.70–2.70), with similar risks across strata of viral loads and immunosuppression. Current and previous diagnoses of tuberculosis were associated with COVID-19 death (aHR, 2.70 [95% CI, 1.81–4.04] and 1.51 [95% CI, 1.18–1.93], respectively). The SMR for COVID-19 death associated with HIV was 2.39 (95% CI, 1.96–2.86); population attributable fraction 8.5% (95% CI, 6.1–11.1)

Measuring the roles universities play in regional innovation systems : a comparative study between Chilean and Canadian natural resource-based regions

Universities can play critical roles in regional industrial development through innovation and entrepreneurship clusters. Formally managing this function in an integrated fashion is not well practiced by many universities. To improve this practice, we define the roles that universities can play and numerical indicators to measure them. Most world regions are 'peripheral' to a few core areas where academic research concentrates. Peripheral regions depend heavily on natural resource industries in both developed and developing countries. Therefore, we study universities involved with wine, salmon culture, mining and eco-tourism, and collect original comparative data from four universities in Canada and four in Chile. They are mostly small schools in peripheral regions, but among the national leaders in involvement with the local resource industry